fit {OUTRIDER} | R Documentation

## Fit the negative binomial distribution

### Description

Fit a negative binomial (NB) distribution to the counts per gene over all samples using, if available, the precomputed control factors. If no normalization factors are provided only the sizeFactors are used.

### Usage

    fit(object, ...)

    ## S4 method for signature 'OutriderDataSet'
    fit(object, BPPARAM = bpparam())

### Arguments

`object` | An OutriderDataSet
`...` | additional arguments, currently not used.
`BPPARAM` | by default bpparam()

### Value

An OutriderDataSet object with the fitted model. Accessible through: `mcols(ods)[,c('mu', 'theta')]`.

### Examples

    ods <- makeExampleOutriderDataSet()
    ods <- estimateSizeFactors(ods)
    ods <- fit(ods)

    mcols(ods)[1:10,c('mu', 'theta')]

[Package OUTRIDER version 1.6.0 Index]